Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
ESPNP	284729	broad.mit.edu	37	1	17023110	17023110	+	Missense_Mutation	SNP	G	A	A	rs11260887	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17023110G>A	uc001azn.1	-	10	1754	c.1640C>T	c.(1639-1641)CCG>CTG	p.P547L		NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						GTTGAGCAGCGGCTGAAACCC	0.687													10	21	---	---	---	---	PASS
CELA3B	23436	broad.mit.edu	37	1	22304925	22304925	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22304925T>A	uc001bfk.2	+	2	222	c.107T>A	c.(106-108)GTC>GAC	p.V36D	CELA3B_uc009vqf.2_Missense_Mutation_p.V35D	NM_007352	NP_031378	P08861	CEL3B_HUMAN	elastase 3B, pancreatic preproprotein	36	Peptidase S1.				cholesterol metabolic process|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1						GAGGATGCGGTCCCCTACAGC	0.622													18	119	---	---	---	---	PASS
ZDHHC18	84243	broad.mit.edu	37	1	27180396	27180396	+	3'UTR	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27180396C>T	uc001bnb.2	+	8						NM_032283	NP_115659	Q9NUE0	ZDH18_HUMAN	zinc finger, DHHC-type containing 18							integral to membrane	zinc ion binding				0		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)		CTGCCGGGACCCTCCCTATTC	0.572													20	70	---	---	---	---	PASS
HDAC1	3065	broad.mit.edu	37	1	32796451	32796451	+	Silent	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32796451C>T	uc001bvb.1	+	9	984	c.921C>T	c.(919-921)AAC>AAT	p.N307N	HDAC1_uc010ohf.1_Silent_p.N278N|HDAC1_uc001bvc.1_Silent_p.N63N	NM_004964	NP_004955	Q13547	HDAC1_HUMAN	histone deacetylase 1	307	Histone deacetylase.				anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	CCATTCGTAACGTTGCCCGGT	0.567													22	95	---	---	---	---	PASS
KIAA1522	57648	broad.mit.edu	37	1	33237800	33237800	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33237800C>T	uc001bvv.2	+	6	2979	c.2843C>T	c.(2842-2844)TCA>TTA	p.S948L	KIAA1522_uc001bvu.1_Missense_Mutation_p.S1007L|KIAA1522_uc010ohm.1_Missense_Mutation_p.S959L|KIAA1522_uc010ohn.1_Intron	NM_020888	NP_065939	Q9P206	K1522_HUMAN	hypothetical protein LOC57648	948	Pro-rich.										0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CGGAGCATCTCAGAGCAGCGG	0.667													9	54	---	---	---	---	PASS
ZMYM6	9204	broad.mit.edu	37	1	35480663	35480663	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35480663T>C	uc001byh.2	-	5	757	c.529A>G	c.(529-531)AAG>GAG	p.K177E	ZMYM6_uc001byf.1_Missense_Mutation_p.K177E|ZMYM6_uc010oht.1_Missense_Mutation_p.K80E|ZMYM6_uc009vup.2_5'UTR|ZMYM6_uc009vuq.1_Missense_Mutation_p.K177E|ZMYM6_uc009vur.1_5'UTR	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258	177	MYM-type 2.				multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				GGTTTTTTCTTTAGCTCATAA	0.348													24	113	---	---	---	---	PASS
ORC1L	4998	broad.mit.edu	37	1	52851529	52851529	+	Silent	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52851529T>A	uc001ctt.2	-	9	1695	c.1476A>T	c.(1474-1476)CGA>CGT	p.R492R	ORC1L_uc010oni.1_Silent_p.R487R|ORC1L_uc001ctu.2_Silent_p.R492R|ORC1L_uc009vzd.2_Silent_p.R246R	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	492					cell cycle checkpoint|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0						AGTACCTCAGTCGGGCTTCCT	0.542													8	43	---	---	---	---	PASS
ZYG11B	79699	broad.mit.edu	37	1	53245634	53245634	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53245634T>A	uc001cuj.2	+	4	1256	c.1061T>A	c.(1060-1062)GTG>GAG	p.V354E	ZYG11B_uc009vzg.2_RNA|ZYG11B_uc010onj.1_Missense_Mutation_p.V345E	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B	354							protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						CTGACTCATGTGATGGAAAAA	0.363													34	197	---	---	---	---	PASS
C1orf83	127428	broad.mit.edu	37	1	54562078	54562078	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54562078G>A	uc001cwt.1	+	5	759	c.559G>A	c.(559-561)GAA>AAA	p.E187K	C1orf83_uc001cwu.1_RNA	NM_153035	NP_694580	Q96MN5	TEAN2_HUMAN	hypothetical protein LOC127428	187	TFIIS central.				transcription, DNA-dependent	nucleus	DNA binding				0						GCACCGAGCTGAAATCCGGGC	0.572													19	129	---	---	---	---	PASS
MIER1	57708	broad.mit.edu	37	1	67450321	67450321	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67450321T>G	uc001dde.2	+	14	1570	c.1436T>G	c.(1435-1437)ATT>AGT	p.I479S	MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Missense_Mutation_p.I443S|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Missense_Mutation_p.I443S|MIER1_uc001ddg.2_Missense_Mutation_p.I399S|MIER1_uc010opg.1_Missense_Mutation_p.I443S|MIER1_uc001ddj.1_Missense_Mutation_p.I426S|MIER1_uc001ddi.2_Intron	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b	450					positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						GGGTTACACATTAATGGACCA	0.353													49	206	---	---	---	---	PASS
DENND2D	79961	broad.mit.edu	37	1	111734915	111734915	+	Silent	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111734915A>C	uc001eak.1	-	8	1019	c.819T>G	c.(817-819)GCT>GCG	p.A273A	DENND2D_uc001eal.1_Silent_p.A270A	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	273	DENN.									ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		GTGCGGCAGCAGCATGGATGC	0.632													9	85	---	---	---	---	PASS
DENND2D	79961	broad.mit.edu	37	1	111734916	111734916	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111734916G>T	uc001eak.1	-	8	1018	c.818C>A	c.(817-819)GCT>GAT	p.A273D	DENND2D_uc001eal.1_Missense_Mutation_p.A270D	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	273	DENN.									ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		TGCGGCAGCAGCATGGATGCA	0.627													9	82	---	---	---	---	PASS
DENND2C	163259	broad.mit.edu	37	1	115137133	115137133	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115137133G>A	uc001efd.1	-	18	3094	c.2392C>T	c.(2392-2394)CGA>TGA	p.R798*	DENND2C_uc001eez.2_RNA|DENND2C_uc001efc.1_Nonsense_Mutation_p.R741*	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	798										skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTTCATTTCGTTCTTCCAAA	0.358													9	229	---	---	---	---	PASS
FMO5	2330	broad.mit.edu	37	1	146672922	146672922	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146672922T>A	uc001epi.2	-	7	1384	c.995A>T	c.(994-996)TAT>TTT	p.Y332F	FMO5_uc001eph.3_Missense_Mutation_p.Y332F|FMO5_uc001epj.2_Intron	NM_001461	NP_001452	P49326	FMO5_HUMAN	flavin containing monooxygenase 5 isoform 1	332						integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			ovary(3)	3	all_hematologic(923;0.0487)					GTCAAAGCTATAGCCTGTGGC	0.438													8	128	---	---	---	---	PASS
S100A14	57402	broad.mit.edu	37	1	153587436	153587436	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153587436C>A	uc001fce.2	-	4	338	c.240G>T	c.(238-240)GAG>GAT	p.E80D	S100A16_uc001fcd.1_5'Flank	NM_020672	NP_065723	Q9HCY8	S10AE_HUMAN	S100 calcium binding protein A14	80	2; high affinity (Potential).				calcium ion homeostasis|defense response to bacterium|positive regulation of granulocyte chemotaxis|positive regulation of monocyte chemotaxis|response to lipopolysaccharide|toll-like receptor 4 signaling pathway	cell junction|microtubule cytoskeleton|perinuclear region of cytoplasm	calcium ion binding|chemokine receptor binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			AACTCCTGAACTCCAGTTTAG	0.557													32	145	---	---	---	---	PASS
GON4L	54856	broad.mit.edu	37	1	155753882	155753882	+	Splice_Site	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155753882T>G	uc001flz.2	-	14	1886	c.1789_splice	c.e14-1	p.F597_splice	GON4L_uc001fly.1_Splice_Site_p.F597_splice|GON4L_uc009wrh.1_Splice_Site_p.F597_splice|GON4L_uc001fma.1_Splice_Site_p.F597_splice|GON4L_uc001fmc.2_Splice_Site_p.F597_splice|GON4L_uc001fmd.3_Splice_Site_p.F597_splice|GON4L_uc009wri.2_Splice_Site_p.F183_splice|GON4L_uc009wrj.1_Splice_Site_p.F112_splice|GON4L_uc001fme.2_Splice_Site_p.F425_splice	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					ATCTTGGAACTGTGGGCAAAG	0.473													34	148	---	---	---	---	PASS
CD1A	909	broad.mit.edu	37	1	158226750	158226750	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158226750G>T	uc001frt.2	+	4	1312	c.779G>T	c.(778-780)TGG>TTG	p.W260L		NM_001763	NP_001754	P06126	CD1A_HUMAN	CD1A antigen precursor	260	Extracellular (Potential).|Ig-like.				antigen processing and presentation|immune response	endosome membrane|integral to plasma membrane|MHC class I protein complex				pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	GATGGGACATGGTATCTCCGC	0.627													5	164	---	---	---	---	PASS
KIAA1614	57710	broad.mit.edu	37	1	180904820	180904820	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180904820A>C	uc001gok.2	+	5	1842	c.1775A>C	c.(1774-1776)GAA>GCA	p.E592A	KIAA1614_uc001gol.1_Missense_Mutation_p.E213A|KIAA1614_uc001gom.1_Intron	NM_020950	NP_066001	Q5VZ46	K1614_HUMAN	hypothetical protein LOC57710	592										ovary(3)|skin(1)	4						CTCCACATGGAATGGATCCGG	0.637													9	58	---	---	---	---	PASS
MARK1	4139	broad.mit.edu	37	1	220752837	220752837	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220752837A>G	uc001hmn.3	+	2	790	c.193A>G	c.(193-195)ACA>GCA	p.T65A	MARK1_uc001hml.2_Missense_Mutation_p.T65A|MARK1_uc009xdw.2_Missense_Mutation_p.T65A|MARK1_uc010pun.1_Missense_Mutation_p.T65A|MARK1_uc001hmm.3_Missense_Mutation_p.T65A	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	65	Protein kinase.				intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)		TTTACAAAAAACAATAGGGAA	0.428													15	111	---	---	---	---	PASS
ASAP2	8853	broad.mit.edu	37	2	9533614	9533614	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9533614C>A	uc002qzh.2	+	24	2862	c.2522C>A	c.(2521-2523)CCC>CAC	p.P841H	ASAP2_uc002qzi.2_Missense_Mutation_p.P796H	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH	841	Pro-rich.				regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						TCCGCAGATCCCCTGACCCCC	0.637													4	32	---	---	---	---	PASS
PQLC3	130814	broad.mit.edu	37	2	11304356	11304356	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11304356C>A	uc002rbc.2	+	4	456	c.323C>A	c.(322-324)GCC>GAC	p.A108D	PQLC3_uc010yjk.1_Missense_Mutation_p.A108D	NM_152391	NP_689604	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3 precursor	108	Helical; (Potential).					integral to membrane					0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		TTCATCCTTGCCCTGCAGAAG	0.453													24	79	---	---	---	---	PASS
MDH1	4190	broad.mit.edu	37	2	63834039	63834039	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63834039T>A	uc002scj.1	+	9	979	c.923T>A	c.(922-924)TTC>TAC	p.F308Y	MDH1_uc010ypv.1_Missense_Mutation_p.F326Y|MDH1_uc010ypw.1_Missense_Mutation_p.F213Y	NM_005917	NP_005908	P40925	MDHC_HUMAN	cytosolic malate dehydrogenase	308					gluconeogenesis|tricarboxylic acid cycle	centrosome|cytosol	L-malate dehydrogenase activity|malic enzyme activity			kidney(2)	2					NADH(DB00157)	ATTAATGATTTCTCACGTGAG	0.353													49	115	---	---	---	---	PASS
ANXA4	307	broad.mit.edu	37	2	70045736	70045736	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70045736G>A	uc002sfr.3	+	10	861	c.634G>A	c.(634-636)GAT>AAT	p.D212N	ANXA4_uc010yqn.1_RNA|ANXA4_uc002sfs.3_Missense_Mutation_p.D190N|ANXA4_uc010yqo.1_Missense_Mutation_p.D128N	NM_001153	NP_001144	P09525	ANXA4_HUMAN	annexin IV	210	Annexin 3.				anti-apoptosis|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity				0						TGCAGTGTTTGATGAATACAA	0.338													39	133	---	---	---	---	PASS
TMEM131	23505	broad.mit.edu	37	2	98418894	98418894	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98418894G>A	uc002syh.3	-	24	2877	c.2648C>T	c.(2647-2649)TCA>TTA	p.S883L		NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	883						integral to membrane				ovary(4)|central_nervous_system(2)	6						TACTTACCTTGATACTAACTT	0.328													20	88	---	---	---	---	PASS
SSFA2	6744	broad.mit.edu	37	2	182766972	182766972	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182766972G>C	uc002uoi.2	+	8	1514	c.1192G>C	c.(1192-1194)GAA>CAA	p.E398Q	SSFA2_uc002uoh.2_Missense_Mutation_p.E398Q|SSFA2_uc002uoj.2_Missense_Mutation_p.E398Q|SSFA2_uc002uok.2_RNA|SSFA2_uc010zfo.1_Missense_Mutation_p.E245Q|SSFA2_uc002uol.2_Missense_Mutation_p.E245Q	NM_001130445	NP_001123917	P28290	SSFA2_HUMAN	sperm specific antigen 2 isoform 1	398						cytoplasm|plasma membrane	actin binding			breast(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			ACAAAGTAAAGAAACTCAAAG	0.363													28	133	---	---	---	---	PASS
NUP35	129401	broad.mit.edu	37	2	184016285	184016285	+	Silent	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184016285A>C	uc002upf.2	+	5	550	c.447A>C	c.(445-447)ACA>ACC	p.T149T	NUP35_uc010zfs.1_Silent_p.T131T|NUP35_uc010zft.1_Silent_p.T31T|NUP35_uc002upg.2_Intron	NM_138285	NP_612142	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa	149					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	intermediate filament cytoskeleton|nuclear membrane|nuclear pore|plasma membrane					0						GAAAGACGACATTATCTCCTG	0.413													25	148	---	---	---	---	PASS
KCTD18	130535	broad.mit.edu	37	2	201354993	201354993	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201354993G>C	uc002uvs.2	-	7	1628	c.1111C>G	c.(1111-1113)CCT>GCT	p.P371A	KCTD18_uc002uvt.2_Missense_Mutation_p.P371A	NM_152387	NP_689600	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain	371						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1						TGGGGTGTAGGCTTCTTGTCG	0.647													40	130	---	---	---	---	PASS
TUBA4A	7277	broad.mit.edu	37	2	220116808	220116808	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220116808T>G	uc002vkt.1	-	2	206	c.148A>C	c.(148-150)ACC>CCC	p.T50P	TUBA4A_uc010zkz.1_Missense_Mutation_p.T35P|TUBA4B_uc002vku.2_5'Flank|TUBA4B_uc002vkv.1_5'Flank	NM_006000	NP_005991	P68366	TBA4A_HUMAN	tubulin, alpha 4a	50					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|platelet activation|platelet degranulation|protein polymerization	cytosol|extracellular region|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)	3		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AAGAAGGTGGTGAAGGAGTCG	0.542													10	69	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238244811	238244811	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238244811C>T	uc002vwl.2	-	40	9217	c.8932G>A	c.(8932-8934)GCT>ACT	p.A2978T	COL6A3_uc002vwo.2_Missense_Mutation_p.A2772T|COL6A3_uc010znj.1_Missense_Mutation_p.A2371T|COL6A3_uc002vwj.2_Missense_Mutation_p.A359T	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2978	Nonhelical region.|Ala-rich.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTGGTGGCAGCTGGTTTGGCT	0.587													13	60	---	---	---	---	PASS
CLASP2	23122	broad.mit.edu	37	3	33725901	33725901	+	Silent	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33725901C>A	uc003cfu.2	-	6	948	c.594G>T	c.(592-594)GTG>GTT	p.V198V	CLASP2_uc010hgb.2_RNA	NM_015097	NP_055912	B2RTR1	B2RTR1_HUMAN	CLIP-associating protein 2	198										ovary(3)|central_nervous_system(1)	4						CTTTTTCTCCCACATGTCTAT	0.318													35	132	---	---	---	---	PASS
ACY1	95	broad.mit.edu	37	3	52012054	52012054	+	Missense_Mutation	SNP	G	A	A	rs140557711	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52012054G>A	uc011bea.1	+	2	347	c.92G>A	c.(91-93)CGC>CAC	p.R31H	ABHD14B_uc003dcn.2_Intron|ABHD14A_uc010hlz.2_Silent_p.S79S|ABHD14A_uc003dco.2_Silent_p.S79S	NM_000666	NP_000657	Q03154	ACY1_HUMAN	aminoacylase 1	Error:Variant_position_missing_in_Q03154_after_alignment					cellular amino acid metabolic process|proteolysis	cytosol	aminoacylase activity|metal ion binding|metallopeptidase activity			breast(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	L-Aspartic Acid(DB00128)	CTGGCAACTCGCCCATCTTTT	0.617													25	53	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121187276	121187276	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121187276G>A	uc003eee.3	-	23	6850	c.6721C>T	c.(6721-6723)CGA>TGA	p.R2241*	POLQ_uc003eed.2_Nonsense_Mutation_p.R1413*	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	2241					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		AAGGTTATTCGTCCTAAAATC	0.333								DNA_polymerases_(catalytic_subunits)					82	167	---	---	---	---	PASS
RBM47	54502	broad.mit.edu	37	4	40428110	40428110	+	Silent	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40428110A>G	uc003gvc.2	-	7	2303	c.1593T>C	c.(1591-1593)ATT>ATC	p.I531I	RBM47_uc003gvd.2_Silent_p.I462I|RBM47_uc003gve.2_RNA|RBM47_uc011bys.1_Silent_p.I493I	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	531	Ala-rich.					nucleus	nucleotide binding|RNA binding			breast(3)	3						CGGCAGTAGGAATTCTCTGAA	0.562													16	86	---	---	---	---	PASS
RASSF6	166824	broad.mit.edu	37	4	74442420	74442420	+	Silent	SNP	A	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74442420A>T	uc003hhd.1	-	9	969	c.846T>A	c.(844-846)ATT>ATA	p.I282I	RASSF6_uc003hhc.1_Silent_p.I250I|RASSF6_uc010iik.1_Silent_p.I216I|RASSF6_uc010iil.1_Silent_p.I238I	NM_201431	NP_958834	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family 6	282	Ras-associating.				apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			GCAGTAGCGGAATGTCTGTCT	0.403													105	406	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113539199	113539199	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113539199G>T	uc003iau.2	-	6	2210	c.1999C>A	c.(1999-2001)CAA>AAA	p.Q667K	C4orf21_uc003iaw.2_Missense_Mutation_p.Q667K	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		CTGACTTCTTGAATAGGTTTA	0.313													13	149	---	---	---	---	PASS
TRIM2	23321	broad.mit.edu	37	4	154229409	154229409	+	Intron	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154229409G>T	uc003ing.2	+						TRIM2_uc003inh.2_Intron|ANXA2P1_uc003inj.2_RNA	NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		GCAACCATCAGCTTGCAGAAG	0.473													4	85	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187549318	187549318	+	Silent	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187549318C>T	uc003izf.2	-	9	4988	c.4800G>A	c.(4798-4800)TCG>TCA	p.S1600S		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	1600	Extracellular (Potential).|Cadherin 14.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						CTGACTCGATCGAGTACAGCA	0.448										HNSCC(5;0.00058)			4	40	---	---	---	---	PASS
IL7R	3575	broad.mit.edu	37	5	35871222	35871222	+	Silent	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35871222G>T	uc003jjs.2	+	4	533	c.444G>T	c.(442-444)GTG>GTT	p.V148V	IL7R_uc011coo.1_Silent_p.V148V|IL7R_uc011cop.1_RNA	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor	148	Extracellular (Potential).|Fibronectin type-III.				immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			ACTTTGTGGTGACATTTAATA	0.388													22	127	---	---	---	---	PASS
DHX29	54505	broad.mit.edu	37	5	54603477	54603477	+	5'UTR	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54603477T>A	uc003jpx.2	-	1					SKIV2L2_uc003jpy.3_5'Flank|SKIV2L2_uc011cqi.1_5'Flank|DHX29_uc010ivw.2_RNA	NM_019030	NP_061903	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29								ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				CTCTTCACATTCCCCGGCTCC	0.652													12	69	---	---	---	---	PASS
PPWD1	23398	broad.mit.edu	37	5	64859225	64859225	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64859225A>T	uc003jtv.3	+	1	95	c.88A>T	c.(88-90)AGA>TGA	p.R30*	PPWD1_uc011cqv.1_Translation_Start_Site|PPWD1_uc011cqw.1_Translation_Start_Site|CENPK_uc003jts.2_5'Flank|CENPK_uc003jtt.2_5'Flank|CENPK_uc003jtu.2_5'Flank	NM_015342	NP_056157	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat	30					protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		ACTCAGCGAAAGAGAGCTGGC	0.567													20	90	---	---	---	---	PASS
SPZ1	84654	broad.mit.edu	37	5	79616637	79616637	+	Silent	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79616637C>T	uc003kgn.2	+	1	848	c.603C>T	c.(601-603)AAC>AAT	p.N201N	uc011ctk.1_RNA	NM_032567	NP_115956	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	201	Basic motif (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(1)	1		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		ACTCTGAGAACACCGCACAAG	0.353													27	99	---	---	---	---	PASS
TCF7	6932	broad.mit.edu	37	5	133451702	133451702	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133451702A>C	uc003kyt.2	+	3	615	c.419A>C	c.(418-420)CAC>CCC	p.H140P	TCF7_uc003kyu.1_Missense_Mutation_p.H25P|TCF7_uc003kyv.2_Missense_Mutation_p.H25P|TCF7_uc003kyw.2_Missense_Mutation_p.H25P|TCF7_uc003kyx.2_5'UTR|TCF7_uc003kyy.2_Missense_Mutation_p.H25P|TCF7_uc003kyz.2_Missense_Mutation_p.H25P|TCF7_uc003kza.2_Missense_Mutation_p.H25P	NM_003202	NP_003193	P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific,	140					cellular response to interleukin-4|immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription regulatory region DNA binding				0		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGGGCAGCACCCCCAGCCG	0.652													6	17	---	---	---	---	PASS
TXNDC15	79770	broad.mit.edu	37	5	134232036	134232036	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134232036G>C	uc003lac.1	+	4	1466	c.808G>C	c.(808-810)GGA>CGA	p.G270R	TXNDC15_uc010jdy.1_RNA|TXNDC15_uc011cxv.1_RNA	NM_024715	NP_078991	Q96J42	TXD15_HUMAN	disulfide isomerase precursor	270	Extracellular (Potential).|Thioredoxin.				cell redox homeostasis	integral to membrane				ovary(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATTATTTCAAGGAGCTAAACC	0.353													46	244	---	---	---	---	PASS
TXNDC15	79770	broad.mit.edu	37	5	134232037	134232037	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134232037G>A	uc003lac.1	+	4	1467	c.809G>A	c.(808-810)GGA>GAA	p.G270E	TXNDC15_uc010jdy.1_RNA|TXNDC15_uc011cxv.1_RNA	NM_024715	NP_078991	Q96J42	TXD15_HUMAN	disulfide isomerase precursor	270	Extracellular (Potential).|Thioredoxin.				cell redox homeostasis	integral to membrane				ovary(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTATTTCAAGGAGCTAAACCA	0.353													48	244	---	---	---	---	PASS
PCDHGB3	56102	broad.mit.edu	37	5	140751901	140751901	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140751901G>A	uc003ljw.1	+	1	1940	c.1940G>A	c.(1939-1941)CGT>CAT	p.R647H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc011dat.1_Missense_Mutation_p.R647H|PCDHGA6_uc011dau.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	647	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCACTGTGCGTGATGGAGGA	0.647													6	50	---	---	---	---	PASS
LARP1	23367	broad.mit.edu	37	5	154179286	154179286	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154179286T>A	uc003lvp.2	+	9	1942	c.1513T>A	c.(1513-1515)TTT>ATT	p.F505I	LARP1_uc003lvo.2_Missense_Mutation_p.F428I|LARP1_uc010jie.1_Missense_Mutation_p.F300I	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	505							protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTGCCCTGAATTTGTTCCCCG	0.517													52	212	---	---	---	---	PASS
PRELID1	27166	broad.mit.edu	37	5	176733119	176733119	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176733119C>G	uc003mfx.2	+	4	605	c.453C>G	c.(451-453)TTC>TTG	p.F151L	RAB24_uc003mfu.2_5'Flank|RAB24_uc003mfv.2_5'Flank|RAB24_uc003mfw.2_5'Flank|PRELID1_uc003mfy.2_Missense_Mutation_p.F149L|MXD3_uc010jkk.2_3'UTR	NM_013237	NP_037369	Q9Y255	PRLD1_HUMAN	PRELI domain containing 1 precursor	151	PRELI/MSF1.				immune response|multicellular organismal development	mitochondrion|nucleus					0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTGCCCGATTCAAAAGCAACG	0.498													28	179	---	---	---	---	PASS
RGS14	10636	broad.mit.edu	37	5	176794983	176794983	+	Intron	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176794983T>G	uc003mgf.2	+						RGS14_uc003mgg.1_Intron|RGS14_uc003mgh.2_Intron|RGS14_uc003mgi.2_5'UTR	NM_006480	NP_006471	O43566	RGS14_HUMAN	regulator of G-protein signalling 14						chromosome segregation|long-term memory|long-term synaptic potentiation|negative regulation of ERK1 and ERK2 cascade|negative regulation of MAP kinase activity|negative regulation of synaptic plasticity|nucleocytoplasmic transport|platelet-derived growth factor receptor signaling pathway|positive regulation of neurogenesis|regulation of DNA-dependent transcription in response to stress|regulation of G-protein coupled receptor protein signaling pathway|response to oxidative stress|spindle organization|visual learning|zygote asymmetric cell division	cell junction|centrosome|dendritic spine|microtubule|PML body|postsynaptic density|postsynaptic membrane|spindle pole	GDP-dissociation inhibitor activity|GTPase activator activity|microtubule binding|receptor signaling complex scaffold activity|receptor signaling protein activity			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTGGTTCGGGTCTTGGGCTAG	0.592													4	5	---	---	---	---	PASS
HIST1H2AK	8330	broad.mit.edu	37	6	27805883	27805883	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27805883T>G	uc003njs.2	-	1	235	c.235A>C	c.(235-237)ATC>CTC	p.I79L	HIST1H2BN_uc003njt.1_5'Flank|HIST1H2BN_uc003nju.1_5'Flank|HIST1H2BN_uc003njv.2_5'Flank	NM_003510	NP_003501	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ak	79					nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding			upper_aerodigestive_tract(1)	1						CGCGGGATGATGCGGGTCTTC	0.627													42	212	---	---	---	---	PASS
CCHCR1	54535	broad.mit.edu	37	6	31111166	31111166	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31111166C>A	uc003nsr.3	-	16	2048	c.1925G>T	c.(1924-1926)CGC>CTC	p.R642L	CCHCR1_uc011dne.1_Missense_Mutation_p.R642L|CCHCR1_uc003nsq.3_Missense_Mutation_p.R695L|CCHCR1_uc003nsp.3_Missense_Mutation_p.R731L	NM_019052	NP_061925	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1 isoform	642	Potential.				cell differentiation|multicellular organismal development	cytoplasm|nucleus	protein binding			skin(1)	1						GGCGGCTCTGCGCTGAATCTG	0.647													21	93	---	---	---	---	PASS
SOBP	55084	broad.mit.edu	37	6	107955403	107955403	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107955403A>G	uc003prx.2	+	6	1859	c.1355A>G	c.(1354-1356)CAC>CGC	p.H452R		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	452	Pro-rich.						metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		AGCCCCATGCACCGGCCCATG	0.751													12	38	---	---	---	---	PASS
HIVEP2	3097	broad.mit.edu	37	6	143081369	143081369	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143081369G>C	uc003qjd.2	-	9	6799	c.6056C>G	c.(6055-6057)CCT>CGT	p.P2019R		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	2019					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CATACAACTAGGTATGTCCAA	0.483													78	248	---	---	---	---	PASS
PRPS1L1	221823	broad.mit.edu	37	7	18066427	18066427	+	3'UTR	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18066427G>C	uc003stz.2	-	1						NM_175886	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like						nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			ovary(1)	1	Lung NSC(10;0.0385)|all_lung(11;0.0736)					ttttaaaataGCATAACCTAG	0.333													57	177	---	---	---	---	PASS
MACC1	346389	broad.mit.edu	37	7	20180463	20180463	+	3'UTR	SNP	G	C	C	rs113938645		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20180463G>C	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						cacacacacagacacacacac	0.164													6	58	---	---	---	---	PASS
OSBPL3	26031	broad.mit.edu	37	7	24874088	24874088	+	Intron	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24874088G>A	uc003sxf.2	-						OSBPL3_uc003sxd.2_RNA|OSBPL3_uc003sxe.2_RNA|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron|OSBPL3_uc003sxj.1_Missense_Mutation_p.S317F|OSBPL3_uc003sxk.1_Missense_Mutation_p.S286F	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						AGTGGCAAGGGAAGGCTGACT	0.617													16	172	---	---	---	---	PASS
PSMA2	5683	broad.mit.edu	37	7	42958801	42958801	+	Intron	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42958801T>C	uc003thy.2	-						C7orf25_uc010kxr.2_Intron|PSMA2_uc010kxt.2_Intron|PSMA2_uc003thz.1_3'UTR	NM_002787	NP_002778	P25787	PSA2_HUMAN	proteasome subunit alpha type 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|response to virus|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	protein binding|threonine-type endopeptidase activity			large_intestine(2)|ovary(1)	3						GGAGACTGGATTGGAACAATT	0.398													20	69	---	---	---	---	PASS
CPSF4	10898	broad.mit.edu	37	7	99047957	99047957	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99047957G>T	uc003uqj.2	+	4	509	c.366G>T	c.(364-366)AAG>AAT	p.K122N	PTCD1_uc011kiw.1_Intron|CPSF4_uc003uqi.2_Missense_Mutation_p.K122N|CPSF4_uc003uqk.2_Missense_Mutation_p.K122N|CPSF4_uc011kix.1_Missense_Mutation_p.K69N	NM_006693	NP_006684	O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4,	122	C3H1-type 4.				modification by virus of host mRNA processing|mRNA processing|viral infectious cycle	mRNA cleavage and polyadenylation specificity factor complex	RNA binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CCAAGATCAAGGACTGTCCTT	0.622													11	82	---	---	---	---	PASS
FAM3C	10447	broad.mit.edu	37	7	121023056	121023056	+	Translation_Start_Site	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121023056A>C	uc003vjx.2	-	2	216	c.-32T>G	c.(-34--30)ATTAA>ATGAA		FAM3C_uc010lkm.2_Translation_Start_Site	NM_014888	NP_055703	Q92520	FAM3C_HUMAN	family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)					ACTTTTCATTAATATGCTCCT	0.303													29	103	---	---	---	---	PASS
NOBOX	135935	broad.mit.edu	37	7	144098145	144098145	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144098145G>C	uc011kue.1	-	4	838	c.838C>G	c.(838-840)CGC>GGC	p.R280G		NM_001080413	NP_001073882	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	280	Homeobox.				cell differentiation|oogenesis	nucleus	sequence-specific DNA binding			ovary(1)	1	Melanoma(164;0.14)					TTACCTGAGCGGTATAGGGTT	0.542													22	91	---	---	---	---	PASS
MNX1	3110	broad.mit.edu	37	7	156803064	156803064	+	5'UTR	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156803064G>A	uc003wnd.1	-	1					MNX1_uc003wmz.2_5'Flank|MNX1_uc003wna.2_5'UTR|MNX1_uc010lqq.1_5'Flank|MNX1_uc003wnc.1_5'Flank|MNX1_uc010lqr.1_5'Flank|uc003wne.1_5'Flank	NM_005515	NP_005506	P50219	MNX1_HUMAN	motor neuron and pancreas homeobox 1 isoform 1						humoral immune response|regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGGGCTGGCGCTCAGGGCCC	0.677									Currarino_syndrome				3	13	---	---	---	---	PASS
NAT2	10	broad.mit.edu	37	8	18258243	18258243	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18258243T>C	uc003wyw.1	+	2	837	c.730T>C	c.(730-732)TTC>CTC	p.F244L		NM_000015	NP_000006	P11245	ARY2_HUMAN	N-acetyltransferase 2	244					xenobiotic metabolic process	cytosol	arylamine N-acetyltransferase activity			ovary(1)|skin(1)	2				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)		CTATAGAAAATTCAATTATAA	0.393									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				42	126	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125072866	125072866	+	Silent	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125072866C>T	uc003yqw.2	+	24	3269	c.3063C>T	c.(3061-3063)TGC>TGT	p.C1021C	uc003yqy.1_RNA	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1021	Cytoplasmic (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TCATTGAGTGCGGAGGACAAG	0.547													23	92	---	---	---	---	PASS
NFKBIL2	4796	broad.mit.edu	37	8	145666428	145666428	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145666428A>T	uc011llg.1	-	8	947	c.932T>A	c.(931-933)ATG>AAG	p.M311K		NM_013432	NP_038460	Q96HA7	TONSL_HUMAN	NF-kappa-B inhibitor-like protein 2	311	TPR 7.				cytoplasmic sequestering of transcription factor|double-strand break repair via homologous recombination|replication fork processing	cytoplasm|nuclear replication fork	histone binding|transcription corepressor activity				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			ACAGATGACCATGGCACCCTG	0.637													37	180	---	---	---	---	PASS
KGFLP2	654466	broad.mit.edu	37	9	41962424	41962424	+	RNA	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:41962424T>A	uc004aca.3	-	3		c.1085A>T				NR_003670				Homo sapiens cDNA FLJ76381 complete cds.												0						GCTTGATCAGTTTTTCAGTAG	0.318													2	2	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	88464343	88464343	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88464343A>C	uc004aoh.1	+	10	1633	c.530A>C	c.(529-531)CAG>CCG	p.Q177P						RecName: Full=Kinesin-like protein KIF27;																		GAACTAGAGCAGAGTGTAGAT	0.363													6	205	---	---	---	---	PASS
OR1L1	26737	broad.mit.edu	37	9	125424612	125424612	+	Silent	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125424612C>T	uc011lza.1	+	1	768	c.768C>T	c.(766-768)GTC>GTT	p.V256V		NM_001005236	NP_001005236	Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L,	256	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(1)	4						GCTTGGCTGTCATAATGACCC	0.398													94	321	---	---	---	---	PASS
CEL	1056	broad.mit.edu	37	9	135942474	135942474	+	Splice_Site	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135942474G>A	uc010naa.1	+	7	803	c.787_splice	c.e7-1	p.V263_splice		NM_001807	NP_001798	P19835	CEL_HUMAN	carboxyl ester lipase precursor						cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification	cytosol|extracellular space	acylglycerol lipase activity|carboxylesterase activity|heparin binding|sterol esterase activity|triglyceride lipase activity			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		TCTGCCCCCAGGTGGCTGAGA	0.597													4	91	---	---	---	---	PASS
LCN1	3933	broad.mit.edu	37	9	138413417	138413417	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138413417A>G	uc004cfz.1	+	1	132	c.74A>G	c.(73-75)GAC>GGC	p.D25G	LCN1_uc004cga.1_Missense_Mutation_p.D25G	NM_002297	NP_002288	P31025	LCN1_HUMAN	lipocalin 1 precursor	25					proteolysis|response to stimulus|sensory perception of taste	extracellular region	cysteine-type endopeptidase inhibitor activity|transporter activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.54e-08)|Epithelial(140;5.25e-08)|all cancers(34;9.27e-07)|READ - Rectum adenocarcinoma(205;0.155)		CTGGCCTCAGACGAGGAGATT	0.662													5	47	---	---	---	---	PASS
PITRM1	10531	broad.mit.edu	37	10	3197825	3197825	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3197825C>T	uc010qah.1	-	13	1515	c.1483G>A	c.(1483-1485)GAG>AAG	p.E495K	PITRM1_uc001igr.1_Missense_Mutation_p.E527K|PITRM1_uc001igt.1_Missense_Mutation_p.E527K|PITRM1_uc009xhv.1_Missense_Mutation_p.E92K|PITRM1_uc001igu.1_Missense_Mutation_p.E519K|PITRM1_uc010qai.1_Missense_Mutation_p.E498K|PITRM1_uc001igw.1_Missense_Mutation_p.E527K			E7ES23	E7ES23_HUMAN	SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;	495					proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1						GACAGAGCCTCGACCTTCTGC	0.557													34	113	---	---	---	---	PASS
LOC100133308	100133308	broad.mit.edu	37	10	45652235	45652235	+	5'Flank	SNP	C	G	G	rs149362183		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45652235C>G	uc009xmq.1	-						uc001jca.3_RNA|uc001jcb.1_RNA|uc009xmr.1_RNA	NR_024472				Homo sapiens cDNA FLJ32851 fis, clone TESTI2003432.												0						GAAGGAACATCTGAAGGAACA	0.338													3	15	---	---	---	---	PASS
CWF19L1	55280	broad.mit.edu	37	10	102006678	102006678	+	Silent	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102006678G>A	uc001kqq.1	-	8	810	c.723C>T	c.(721-723)TTC>TTT	p.F241F	CWF19L1_uc001kqs.1_5'UTR|CWF19L1_uc001kqr.1_Silent_p.F241F|CWF19L1_uc001kqt.1_5'UTR|CWF19L1_uc010qpn.1_Silent_p.F104F	NM_018294	NP_060764	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control	241							catalytic activity				0		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		GAACAATACTGAACGCGTAAA	0.393													19	80	---	---	---	---	PASS
GTF2H1	2965	broad.mit.edu	37	11	18357301	18357301	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18357301G>T	uc001moi.2	+	4	849	c.155G>T	c.(154-156)TGC>TTC	p.C52F	GTF2H1_uc001moh.2_Missense_Mutation_p.C52F|GTF2H1_uc009yhm.2_Intron	NM_001142307	NP_001135779	P32780	TF2H1_HUMAN	general transcription factor IIH, polypeptide 1,	52					mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	protein binding				0						TTCTTTTTAGGCCAGAAAATT	0.423								NER					13	76	---	---	---	---	PASS
MFRP	83552	broad.mit.edu	37	11	119212284	119212284	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119212284C>A	uc001pwj.2	-	13	1874	c.1714G>T	c.(1714-1716)GAC>TAC	p.D572Y	MFRP_uc010rzf.1_RNA|MFRP_uc010rzg.1_Missense_Mutation_p.D454Y	NM_031433	NP_113621	Q9BXJ0	C1QT5_HUMAN	membrane frizzled-related protein	Error:Variant_position_missing_in_Q9BXJ0_after_alignment						collagen					0		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		GCTTCCAGGTCAGCTGCCTCT	0.662													12	41	---	---	---	---	PASS
THYN1	29087	broad.mit.edu	37	11	134118717	134118717	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134118717T>C	uc001qhf.2	-	7	719	c.617A>G	c.(616-618)CAG>CGG	p.Q206R	THYN1_uc001qhg.2_Missense_Mutation_p.Q206R|THYN1_uc001qhh.2_Missense_Mutation_p.Q206R|THYN1_uc001qhi.2_Intron|THYN1_uc001qhj.2_Intron	NM_001037305	NP_001032382	Q9P016	THYN1_HUMAN	thymocyte nuclear protein 1 isoform 1	206						nucleus					0	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;1.68e-10)|all cancers(11;1.95e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00148)|Lung(977;0.207)		ggtcagggGCTGGATTGATAA	0.234													7	114	---	---	---	---	PASS
DIP2B	57609	broad.mit.edu	37	12	51084867	51084867	+	Silent	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51084867T>C	uc001rwv.2	+	13	1743	c.1587T>C	c.(1585-1587)GTT>GTC	p.V529V	DIP2B_uc009zlt.2_Intron	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B	529						nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						TAATGGGAGTTACAGTATCCC	0.383													39	126	---	---	---	---	PASS
ESPL1	9700	broad.mit.edu	37	12	53684167	53684167	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53684167A>T	uc001sck.2	+	24	5369	c.5278A>T	c.(5278-5280)ATC>TTC	p.I1760F	ESPL1_uc001scj.2_Missense_Mutation_p.I1435F	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1760					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						GTTTGATGCCATCCAGAAGGC	0.547													25	94	---	---	---	---	PASS
HOXC6	3223	broad.mit.edu	37	12	54422672	54422672	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54422672T>C	uc001sev.2	+	1	479	c.367T>C	c.(367-369)TAC>CAC	p.Y123H	HOXC6_uc001ses.2_Missense_Mutation_p.Y41H|HOXC5_uc001set.2_Intron|HOXC4_uc001seu.2_Intron	NM_004503	NP_004494	P09630	HXC6_HUMAN	homeobox C6 isoform 1	123	Antp-type hexapeptide.				regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|upper_aerodigestive_tract(1)	3						TATCCAGATTTACCCCTGGAT	0.468													39	282	---	---	---	---	PASS
ATP5B	506	broad.mit.edu	37	12	57033957	57033957	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57033957T>C	uc001slr.2	-	8	1199	c.1094A>G	c.(1093-1095)GAT>GGT	p.D365G		NM_001686	NP_001677	P06576	ATPB_HUMAN	mitochondrial ATP synthase beta subunit	365					angiogenesis|ATP hydrolysis coupled proton transport|regulation of intracellular pH|respiratory electron transport chain	cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)	1						AGTCAAGTCATCAGCAGGCAC	0.398													14	67	---	---	---	---	PASS
PPFIA2	8499	broad.mit.edu	37	12	81675169	81675169	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81675169C>T	uc001szo.1	-	27	3240	c.3079G>A	c.(3079-3081)GAA>AAA	p.E1027K	PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_RNA|PPFIA2_uc010suh.1_RNA|PPFIA2_uc010sui.1_RNA|PPFIA2_uc010suj.1_RNA|PPFIA2_uc009zsi.1_RNA|PPFIA2_uc010suf.1_RNA|PPFIA2_uc009zsh.2_RNA	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2	926										ovary(3)|lung(2)|pancreas(1)	6						GGAAGCCATTCATTTCCAATC	0.393													33	171	---	---	---	---	PASS
BRAP	8315	broad.mit.edu	37	12	112121089	112121089	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112121089C>G	uc001tsn.3	-	2	299	c.105G>C	c.(103-105)GAG>GAC	p.E35D	BRAP_uc010syh.1_5'Flank|BRAP_uc009zvv.2_Missense_Mutation_p.E5D|ACAD10_uc009zvw.2_5'Flank|ACAD10_uc001tso.3_5'Flank|ACAD10_uc001tsp.2_5'Flank|ACAD10_uc009zvx.2_5'Flank|ACAD10_uc001tsq.2_5'Flank	NM_006768	NP_006759	Q7Z569	BRAP_HUMAN	BRCA1 associated protein	35					MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1						TCTTTTTTATCTCCTCATCAG	0.423													7	339	---	---	---	---	PASS
SMAD9	4093	broad.mit.edu	37	13	37453538	37453538	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37453538G>A	uc001uvw.2	-	2	632	c.289C>T	c.(289-291)CGC>TGC	p.R97C	SMAD9_uc001uvx.2_Missense_Mutation_p.R97C|SMAD9_uc010tep.1_5'UTR	NM_001127217	NP_001120689	O15198	SMAD9_HUMAN	SMAD family member 9 isoform a	97	MH1.				BMP signaling pathway|transforming growth factor beta receptor signaling pathway	cytosol|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		TCCGGCCAGCGCCACACGCGA	0.612													21	66	---	---	---	---	PASS
FAM124A	220108	broad.mit.edu	37	13	51825776	51825776	+	Silent	SNP	G	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51825776G>T	uc001vfg.1	+	3	404	c.273G>T	c.(271-273)CGG>CGT	p.R91R	FAM124A_uc001vfe.2_Silent_p.R91R|FAM124A_uc001vff.1_Silent_p.R127R	NM_145019	NP_659456	Q86V42	F124A_HUMAN	hypothetical protein LOC220108	91										central_nervous_system(1)	1		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		GGCGGCGGCGGAAGCCCCCCA	0.706													3	3	---	---	---	---	PASS
IPO4	79711	broad.mit.edu	37	14	24651164	24651164	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24651164T>G	uc001wmv.1	-	26	2935	c.2804A>C	c.(2803-2805)CAG>CCG	p.Q935P	IPO4_uc001wmt.1_Missense_Mutation_p.Q413P|IPO4_uc001wmu.2_Missense_Mutation_p.Q597P|IPO4_uc001wmx.1_Missense_Mutation_p.Q799P|IPO4_uc001wmy.1_Missense_Mutation_p.Q799P|IPO4_uc010tnz.1_RNA|IPO4_uc001wmw.1_RNA|IPO4_uc001wmz.1_Missense_Mutation_p.Q935P	NM_024658	NP_078934	Q8TEX9	IPO4_HUMAN	importin 4	935					intracellular protein transport	cytoplasm|nucleus	protein binding|protein transporter activity			kidney(1)	1				GBM - Glioblastoma multiforme(265;0.0087)		AGGATACTCCTGGGCAGGGTG	0.652													22	59	---	---	---	---	PASS
SSTR1	6751	broad.mit.edu	37	14	38678641	38678641	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38678641C>A	uc001wul.1	+	3	664	c.47C>A	c.(46-48)CCC>CAC	p.P16H	SSTR1_uc010amu.1_RNA	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	16	Extracellular (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity			central_nervous_system(3)|ovary(1)|lung(1)	5	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)	TCTCCTAGCCCCAGCCCGGGC	0.731													5	11	---	---	---	---	PASS
FSIP1	161835	broad.mit.edu	37	15	40068678	40068678	+	Silent	SNP	T	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40068678T>A	uc001zki.2	-	2	266	c.48A>T	c.(46-48)TCA>TCT	p.S16S		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	16										ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TTCTTGAATTTGAAGCTGGTT	0.358													48	211	---	---	---	---	PASS
ITPKA	3706	broad.mit.edu	37	15	41793700	41793700	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41793700C>T	uc001znz.2	+	2	540	c.529C>T	c.(529-531)CCG>TCG	p.P177S		NM_002220	NP_002211	P23677	IP3KA_HUMAN	1D-myo-inositol-trisphosphate 3-kinase A	177					signal transduction		ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity				0		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		GGTCAATCTGCCGGTCATAAG	0.612													3	43	---	---	---	---	PASS
MYO5A	4644	broad.mit.edu	37	15	52646191	52646191	+	Silent	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52646191T>G	uc002aby.2	-	26	3688	c.3444A>C	c.(3442-3444)GTA>GTC	p.V1148V	MYO5A_uc002abx.3_Silent_p.V1148V|MYO5A_uc010ugd.1_5'Flank|MYO5A_uc002aca.1_5'Flank|MYO5A_uc002acb.1_5'Flank|MYO5A_uc002acc.1_5'Flank	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	1148	Potential.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		TGTCCAGAGGTACCTTCTTCT	0.443													39	171	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	63000819	63000819	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63000819G>C	uc002alb.3	+	18	2291	c.2291G>C	c.(2290-2292)AGT>ACT	p.S764T		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	764					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						ACTACCGATAGTGAGCTCCTG	0.652													22	53	---	---	---	---	PASS
ABCC6	368	broad.mit.edu	37	16	16284071	16284071	+	Missense_Mutation	SNP	C	T	T	rs140045277		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16284071C>T	uc002den.3	-	12	1622	c.1585G>A	c.(1585-1587)GGC>AGC	p.G529S	ABCC6_uc010bvo.2_RNA|ABCC6_uc010uzz.1_Missense_Mutation_p.G541S	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	529	ABC transmembrane type-1 1.|Cytoplasmic (By similarity).				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		AAGAGGAGGCCGGAGGTCCGC	0.592													29	152	---	---	---	---	PASS
PLA2G15	23659	broad.mit.edu	37	16	68283347	68283347	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68283347C>G	uc002evr.2	+	2	365	c.282C>G	c.(280-282)ATC>ATG	p.I94M	PLA2G15_uc010vld.1_Missense_Mutation_p.I94M|PLA2G15_uc010vle.1_Intron|PLA2G15_uc010vlf.1_Intron	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)	94				I -> T (in Ref. 4; BAD96510).	fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1						TTGACAATATCAGGTGGGGGC	0.547													18	117	---	---	---	---	PASS
FANCA	2175	broad.mit.edu	37	16	89838183	89838183	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89838183C>T	uc002fou.1	-	23	2096	c.2054G>A	c.(2053-2055)AGG>AAG	p.R685K	FANCA_uc010vpn.1_Missense_Mutation_p.R685K	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform	685					DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CAGGACAGCCCTCAGTCTTTC	0.517			D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				33	161	---	---	---	---	PASS
ALOX12B	242	broad.mit.edu	37	17	7990740	7990740	+	Silent	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7990740C>T	uc002gjy.1	-	1	282	c.21G>A	c.(19-21)AGG>AGA	p.R7R	hsa-mir-4314|MI0015846_5'Flank	NM_001139	NP_001130	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	7	PLAT.				epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0						CTGTGGCCACCCTGACTTTGT	0.602										Multiple Myeloma(8;0.094)			27	109	---	---	---	---	PASS
RARA	5914	broad.mit.edu	37	17	38506145	38506145	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38506145A>G	uc002huk.1	+	4	892	c.437A>G	c.(436-438)CAG>CGG	p.Q146R	RARA_uc002hul.3_Missense_Mutation_p.Q146R|RARA_uc010wfe.1_Intron|RARA_uc002hun.1_Missense_Mutation_p.Q141R	NM_000964	NP_000955	P10276	RARA_HUMAN	retinoic acid receptor, alpha isoform 1	146	Nuclear receptor.|NR C4-type.				apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	cytoplasm|nucleoplasm	chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	TGCCGACTGCAGAAGTGCTTT	0.577			T	PML|ZNF145|TIF1|NUMA1|NPM1	APL								22	55	---	---	---	---	PASS
DHX8	1659	broad.mit.edu	37	17	41585811	41585811	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41585811A>G	uc002idu.1	+	16	2498	c.2425A>G	c.(2425-2427)ATC>GTC	p.I809V	DHX8_uc010wif.1_Missense_Mutation_p.I718V|DHX8_uc010wig.1_Missense_Mutation_p.I809V	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	809	Helicase C-terminal.					catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		AGAGTTAATTATCCTCCCAGT	0.468													36	132	---	---	---	---	PASS
EME1	146956	broad.mit.edu	37	17	48452557	48452557	+	5'UTR	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48452557A>C	uc002iqs.1	+	2					MRPL27_uc002iqq.2_5'Flank|MRPL27_uc002iqr.2_5'Flank|EME1_uc010dbp.1_5'UTR	NM_152463	NP_689676	Q96AY2	EME1_HUMAN	essential meiotic endonuclease 1 homolog 1						DNA recombination|DNA repair	nucleolus	DNA binding|endonuclease activity|metal ion binding|protein binding				0	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			GAATTATTTGATAGCACATAC	0.413								Direct_reversal_of_damage|Homologous_recombination					25	108	---	---	---	---	PASS
EME1	146956	broad.mit.edu	37	17	48452559	48452559	+	Translation_Start_Site	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48452559A>G	uc002iqs.1	+	2	63	c.-10A>G	c.(-12--8)ATAGC>ATGGC		MRPL27_uc002iqq.2_5'Flank|MRPL27_uc002iqr.2_5'Flank|EME1_uc010dbp.1_Translation_Start_Site	NM_152463	NP_689676	Q96AY2	EME1_HUMAN	essential meiotic endonuclease 1 homolog 1						DNA recombination|DNA repair	nucleolus	DNA binding|endonuclease activity|metal ion binding|protein binding				0	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			ATTATTTGATAGCACATACTG	0.418								Direct_reversal_of_damage|Homologous_recombination					27	112	---	---	---	---	PASS
INTS2	57508	broad.mit.edu	37	17	60004006	60004006	+	Silent	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60004006T>G	uc002izn.2	-	2	100	c.24A>C	c.(22-24)ATA>ATC	p.I8I	INTS2_uc002izm.2_5'UTR	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	8					snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3						ATTCAGTCATTATTACTGTTT	0.358													9	13	---	---	---	---	PASS
SERPINB7	8710	broad.mit.edu	37	18	61463591	61463591	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61463591A>G	uc002ljl.2	+	5	524	c.428A>G	c.(427-429)AAT>AGT	p.N143S	SERPINB7_uc002ljm.2_Missense_Mutation_p.N143S|SERPINB7_uc010xet.1_Missense_Mutation_p.N126S|SERPINB7_uc010dqg.2_Missense_Mutation_p.N143S	NM_001040147	NP_001035237	O75635	SPB7_HUMAN	serine (or cysteine) proteinase inhibitor, clade	143					regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			lung(2)|central_nervous_system(1)	3		Esophageal squamous(42;0.129)				CGTAATATTAATAAGTGGGTT	0.353													19	95	---	---	---	---	PASS
FZR1	51343	broad.mit.edu	37	19	3522955	3522955	+	5'UTR	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3522955C>A	uc010dtk.2	+	1					FZR1_uc002lxt.2_5'UTR|FZR1_uc002lxv.2_5'UTR	NM_001136198	NP_001129670	Q9UM11	FZR_HUMAN	Fzr1 protein isoform 1						activation of anaphase-promoting complex activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|DNA repair|G2/M transition DNA damage checkpoint|mitosis|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding			lung(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGCTGCAGGCTAACCTTGCC	0.677													29	110	---	---	---	---	PASS
ZNF799	90576	broad.mit.edu	37	19	12491779	12491779	+	Silent	SNP	T	C	C	rs17706075	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12491779T>C	uc002mts.3	-	4	763	c.297A>G	c.(295-297)GCA>GCG	p.A99A				Q96GE5	ZN799_HUMAN	Homo sapiens cDNA clone IMAGE:30340957, **** WARNING: chimeric clone ****.	205	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6						GCCAGAAAAATGCTTTCCCAC	0.388													4	144	---	---	---	---	PASS
ZNF737	100129842	broad.mit.edu	37	19	20727828	20727828	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20727828T>C	uc002npa.2	-	4	1361	c.1181A>G	c.(1180-1182)GAG>GGG	p.E394G		NM_001159293	NP_001152765	C9JHM3	C9JHM3_HUMAN	zinc finger protein 737	394					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						GTAGGGTTTCTCTCCAGTATG	0.408													13	111	---	---	---	---	PASS
CHST8	64377	broad.mit.edu	37	19	34262927	34262927	+	Silent	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34262927C>T	uc002nus.3	+	5	739	c.234C>T	c.(232-234)GAC>GAT	p.D78D	CHST8_uc002nut.3_Silent_p.D78D|CHST8_uc002nuu.2_Silent_p.D78D	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)	78	Lumenal (Potential).				carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)					TCACTCGGGACTTATCCAGTG	0.657													7	108	---	---	---	---	PASS
C19orf41	126123	broad.mit.edu	37	19	50657881	50657881	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50657881A>C	uc002prp.1	-	6	686	c.599T>G	c.(598-600)TTT>TGT	p.F200C		NM_152358	NP_689571	Q6UXV1	IZUM2_HUMAN	hypothetical protein LOC126123 precursor	200	Helical; (Potential).					integral to membrane					0		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00364)|OV - Ovarian serous cystadenocarcinoma(262;0.0052)		CACGAAGACAAAGACAGCCAG	0.602													27	134	---	---	---	---	PASS
LILRB5	10990	broad.mit.edu	37	19	54758770	54758770	+	Silent	SNP	G	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54758770G>C	uc002qex.2	-	6	1194	c.1083C>G	c.(1081-1083)GCC>GCG	p.A361A	LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Silent_p.A352A|LILRB5_uc002qey.2_Silent_p.A361A|LILRB5_uc002qez.2_Silent_p.A261A|LILRB5_uc002qfa.1_Silent_p.A251A|LILRB5_uc010yes.1_RNA	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	361	Ig-like C2-type 4.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCGGGGGATGGGCTGCCCCCT	0.552													19	101	---	---	---	---	PASS
FIZ1	84922	broad.mit.edu	37	19	56109181	56109181	+	Silent	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56109181G>A	uc002qli.3	-	2	141	c.51C>T	c.(49-51)GCC>GCT	p.A17A	FIZ1_uc002qlj.3_Silent_p.A17A|ZNF524_uc002qlk.1_5'Flank	NM_032836	NP_116225	Q96SL8	FIZ1_HUMAN	FLT3-interacting zinc finger 1	17					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|protein kinase binding|receptor binding|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CCCTGGGGGCGGCAGCGGCGG	0.672													10	34	---	---	---	---	PASS
NCOA5	57727	broad.mit.edu	37	20	44693847	44693847	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44693847C>A	uc002xrd.2	-	5	1178	c.650G>T	c.(649-651)GGG>GTG	p.G217V	NCOA5_uc002xrc.2_Missense_Mutation_p.G105V|NCOA5_uc002xre.2_Missense_Mutation_p.G217V	NM_020967	NP_066018	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	217					regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding			central_nervous_system(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)				CACCTTCCGCCCCACAGACTC	0.493													48	199	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62599261	62599261	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62599261A>T	uc002yhl.1	-	2	97	c.43T>A	c.(43-45)TCC>ACC	p.S15T		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	15					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTCTTGCTGGACCCCGGGAGC	0.602													21	125	---	---	---	---	PASS
TMPRSS15	5651	broad.mit.edu	37	21	19666661	19666661	+	Silent	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19666661A>G	uc002ykw.2	-	21	2443	c.2412T>C	c.(2410-2412)TAT>TAC	p.Y804Y		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	804	Extracellular (Potential).|Peptidase S1.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						GTCGGCCGCCATAATACAGAC	0.557													33	193	---	---	---	---	PASS
GCFC1	94104	broad.mit.edu	37	21	34143766	34143766	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34143766C>T	uc002yqn.2	-	1	404	c.214G>A	c.(214-216)GGG>AGG	p.G72R	GCFC1_uc002yqo.2_RNA|GCFC1_uc002yqp.2_Missense_Mutation_p.G72R|GCFC1_uc002yqr.2_Missense_Mutation_p.G72R|C21orf49_uc002yqs.2_5'Flank|C21orf49_uc002yqu.3_5'Flank|C21orf49_uc002yqt.2_5'Flank	NM_016631	NP_057715	Q9Y5B6	GCFC1_HUMAN	GC-rich sequence DNA-binding factor candidate	72						cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						GCCTCAGCCCCGAGGCCCGGG	0.801													3	12	---	---	---	---	PASS
GCFC1	94104	broad.mit.edu	37	21	34143767	34143767	+	Silent	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34143767G>A	uc002yqn.2	-	1	403	c.213C>T	c.(211-213)CTC>CTT	p.L71L	GCFC1_uc002yqo.2_RNA|GCFC1_uc002yqp.2_Silent_p.L71L|GCFC1_uc002yqr.2_Silent_p.L71L|C21orf49_uc002yqs.2_5'Flank|C21orf49_uc002yqu.3_5'Flank|C21orf49_uc002yqt.2_5'Flank	NM_016631	NP_057715	Q9Y5B6	GCFC1_HUMAN	GC-rich sequence DNA-binding factor candidate	71						cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						CCTCAGCCCCGAGGCCCGGGG	0.801													3	8	---	---	---	---	PASS
RCAN1	1827	broad.mit.edu	37	21	35893901	35893901	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35893901A>T	uc002yue.2	-	3	554	c.482T>A	c.(481-483)CTG>CAG	p.L161Q	RCAN1_uc002yuc.2_Missense_Mutation_p.L80Q|RCAN1_uc002yud.2_Missense_Mutation_p.L26Q|RCAN1_uc002yub.2_Missense_Mutation_p.L106Q|RCAN1_uc011adx.1_Missense_Mutation_p.L106Q	NM_004414	NP_004405	P53805	RCAN1_HUMAN	calcipressin 1 isoform a	161					blood circulation|calcium-mediated signaling|central nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						AGGGGAGATCAGAAACTGCTT	0.512													7	43	---	---	---	---	PASS
EWSR1	2130	broad.mit.edu	37	22	29686353	29686353	+	Intron	SNP	T	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29686353T>G	uc003aet.2	+						EWSR1_uc003aes.3_Intron|EWSR1_uc003aev.2_Intron|EWSR1_uc003aew.2_Intron|EWSR1_uc003aex.2_Intron|EWSR1_uc003aey.2_Intron|EWSR1_uc003aez.2_5'UTR	NM_005243	NP_005234	Q01844	EWS_HUMAN	Ewing sarcoma breakpoint region 1 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding		EWSR1/FLI1(2266)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2)	bone(2526)|soft_tissue(702)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|lung(1)|ovary(1)	3254						TCATTGGCTGTTAAACGTGGA	0.373			T	FLI1|ERG|ZNF278|NR4A3|FEV|ATF1|ETV1|ETV4|WT1|ZNF384|CREB1|POU5F1| PBX1	Ewing sarcoma| desmoplastic small round cell tumor |ALL|clear cell sarcoma|sarcoma|myoepithelioma								8	13	---	---	---	---	PASS
GGA1	26088	broad.mit.edu	37	22	38010280	38010280	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38010280G>A	uc003atc.2	+	2	492	c.127G>A	c.(127-129)GGG>AGG	p.G43R	GGA1_uc003atb.2_Missense_Mutation_p.G43R|GGA1_uc003atd.2_Missense_Mutation_p.G43R|GGA1_uc003ate.2_Missense_Mutation_p.G43R|GGA1_uc003atf.2_5'UTR	NM_013365	NP_037497	Q9UJY5	GGA1_HUMAN	golgi associated, gamma adaptin ear containing,	43	VHS.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|Golgi apparatus part	protein binding			breast(2)|ovary(1)	3	Melanoma(58;0.0574)					GGACTTTGAGGGGTAGGTGGC	0.592													20	102	---	---	---	---	PASS
PDXP	57026	broad.mit.edu	37	22	38055358	38055358	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38055358C>G	uc003atm.1	+	1	622	c.569C>G	c.(568-570)ACC>AGC	p.T190S	SH3BP1_uc003atj.1_Intron|uc003atl.1_5'Flank	NM_020315	NP_064711	Q96GD0	PLPP_HUMAN	pyridoxal phosphatase	190					actin rod assembly|cellular response to ATP|positive regulation of actin filament depolymerization|protein dephosphorylation|regulation of cytokinesis|regulation of mitosis	cytosol	heat shock protein binding|metal ion binding|phosphoprotein phosphatase activity|pyridoxal phosphatase activity			ovary(2)	2	Melanoma(58;0.0574)				Pyridoxal(DB00147)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)	GGCAGCCGGACCCCTGGTGAG	0.711													6	26	---	---	---	---	PASS
H1F0	3005	broad.mit.edu	37	22	38201974	38201974	+	Silent	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38201974C>A	uc003aty.2	+	1	861	c.423C>A	c.(421-423)ACC>ACA	p.T141T	GCAT_uc003atz.2_5'Flank|GCAT_uc003aua.1_5'Flank	NM_005318	NP_005309	P07305	H10_HUMAN	H1 histone family, member 0	141					DNA fragmentation involved in apoptotic nuclear change|nucleosome assembly	actin cytoskeleton|Golgi apparatus|nucleoplasm|nucleosome	DNA binding				0	Melanoma(58;0.045)					CCAAAGCCACCCCGGTCAAGA	0.532													25	104	---	---	---	---	PASS
FAM104B	90736	broad.mit.edu	37	X	55172537	55172537	+	Intron	SNP	G	A	A	rs1047054	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55172537G>A	uc004duh.1	-						FAM104B_uc004dug.1_Intron|FAM104B_uc004dui.3_Nonsense_Mutation_p.R111*	NM_138362	NP_612371	Q5XKR9	F104B_HUMAN	hypothetical protein LOC90736												0						GCTTGCCCTCGCTGCTGCAGG	0.438													3	33	---	---	---	---	PASS
THOC2	57187	broad.mit.edu	37	X	122758390	122758390	+	Splice_Site	SNP	A	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122758390A>G	uc004etu.2	-	26	3218	c.3186_splice	c.e26+1	p.K1062_splice	THOC2_uc010nqt.1_5'Flank|THOC2_uc004etw.1_5'Flank	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2						intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3						TATTAGTCATACCTTTTCATA	0.358													61	114	---	---	---	---	PASS
USP26	83844	broad.mit.edu	37	X	132161721	132161721	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132161721C>A	uc010nrm.1	-	6	998	c.528G>T	c.(526-528)CAG>CAT	p.Q176H	USP26_uc011mvf.1_Missense_Mutation_p.Q176H	NM_031907	NP_114113	Q9BXU7	UBP26_HUMAN	ubiquitin-specific protease 26	176					protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(3)|central_nervous_system(3)|kidney(1)|liver(1)	8	Acute lymphoblastic leukemia(192;0.000127)					TCTTCTTGTGCTGATTTTCTG	0.383													49	94	---	---	---	---	PASS
C1orf43	25912	broad.mit.edu	37	1	154192224	154192225	+	Intron	INS	-	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154192224_154192225insA	uc001fei.2	-						C1orf43_uc001feg.2_Intron|C1orf43_uc001feh.2_Intron|C1orf43_uc001fej.2_Intron|C1orf43_uc009wos.1_Intron|C1orf43_uc001fek.2_Intron|C1orf43_uc001fel.2_Intron|UBAP2L_uc009wot.2_5'Flank|UBAP2L_uc010pek.1_5'Flank|UBAP2L_uc001fep.3_5'Flank|UBAP2L_uc010pel.1_5'Flank|UBAP2L_uc001fen.1_5'Flank|UBAP2L_uc010pem.1_5'Flank	NM_001098616	NP_001092086	Q9BWL3	CA043_HUMAN	hypothetical protein LOC25912 isoform 3							integral to membrane	coenzyme binding|oxidoreductase activity				0	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)					ACATGAGAATTAAAGTCATCAC	0.450													20	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	169721614	169721615	+	IGR	INS	-	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169721614_169721615insT								NOSTRIN (50 upstream) : SPC25 (5787 downstream)																							TGTCACAGCACTTTGCATTCAT	0.381													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	242823791	242823791	+	IGR	DEL	T	-	-	rs113052758	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242823791delT								C2orf85 (8309 upstream) : LOC728323 (207053 downstream)																							tgtgtgtgtgtgGCTGGACAG	0.567													4	2	---	---	---	---	
C3orf62	375341	broad.mit.edu	37	3	49308392	49308392	+	3'UTR	DEL	A	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49308392delA	uc003cwn.2	-	3					C3orf62_uc003cwm.2_3'UTR	NM_198562	NP_940964	Q6ZUJ4	CC062_HUMAN	hypothetical protein LOC375341												0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AAGGAAAGTTAAAAAAAAAAA	0.368													3	4	---	---	---	---	
IQCG	84223	broad.mit.edu	37	3	197671126	197671126	+	Intron	DEL	T	-	-	rs74574846		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197671126delT	uc003fyo.2	-						IQCG_uc003fyp.2_Intron|IQCG_uc003fyq.3_Intron	NM_001134435	NP_001127907	Q9H095	IQCG_HUMAN	IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		CAACTTACTCttttttttttt	0.189													4	2	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7726207	7726208	+	Intron	INS	-	TGA	TGA	rs147164731		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7726207_7726208insTGA	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						ggtgatggtggtgatggtggtg	0.000													3	3	---	---	---	---	
FAM13A	10144	broad.mit.edu	37	4	89941431	89941432	+	Intron	INS	-	T	T			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89941431_89941432insT	uc003hse.1	-						FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsh.1_Intron|FAM13A_uc003hsi.2_Intron|FAM13A_uc003hsj.2_Intron	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						TTTTTCTGCCCTTttttttttt	0.114													3	3	---	---	---	---	
DAPP1	27071	broad.mit.edu	37	4	100774533	100774534	+	Intron	DEL	CT	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100774533_100774534delCT	uc003hvf.3	+						DAPP1_uc011cek.1_Intron|DAPP1_uc010ilh.2_Intron	NM_014395	NP_055210	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and						signal transduction	cytoplasm|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein tyrosine phosphatase activity				0				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		TGACCACAAGCTCTCTCCCTGT	0.396													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111322463	111322464	+	IGR	INS	-	TCCTTCCTTCCTTCCTTCCTTCCA	TCCTTCCTTCCTTCCTTCCTTCCA			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111322463_111322464insTCCTTCCTTCCTTCCTTCCTTCCA								ELOVL6 (202643 upstream) : ENPEP (74765 downstream)																							ATttccttccctccttccttcc	0.183													3	3	---	---	---	---	
PBX2	5089	broad.mit.edu	37	6	32157697	32157697	+	5'UTR	DEL	G	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32157697delG	uc003oav.1	-	1					PBX2_uc003oaw.2_5'UTR	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2								transcription factor binding			ovary(1)	1						GTCCATAGCTGGGGGGGGGCC	0.602													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25417776	25417791	+	IGR	DEL	TCCTTCCTCCCTTCCC	-	-	rs144541468	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25417776_25417791delTCCTTCCTCCCTTCCC								NPVF (149671 upstream) : MIR148A (571748 downstream)																							cttccttccttccttcctcccttccctccttccttc	0.000													4	3	---	---	---	---	
PHKG1	5260	broad.mit.edu	37	7	56150799	56150800	+	Intron	DEL	AA	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56150799_56150800delAA	uc003trz.1	-						PSPH_uc003trj.2_Intron|PHKG1_uc003try.1_Intron|PHKG1_uc011kdb.1_Intron|PHKG1_uc011kdc.1_Intron|PHKG1_uc011kdd.1_Intron	NM_006213	NP_006204	Q16816	PHKG1_HUMAN	phosphorylase kinase gamma subunit 1						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	ATP binding|calmodulin binding|phosphorylase kinase activity			large_intestine(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			actccatctcaaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	79183361	79183371	+	IGR	DEL	AAGGAAGGAAG	-	-	rs59835367		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79183361_79183371delAAGGAAGGAAG								GCNT1 (61031 upstream) : PRUNE2 (42922 downstream)																							ggaaggaagaaaggaaggaagaagaaagaaa	0.000													4	2	---	---	---	---	
C9orf114	51490	broad.mit.edu	37	9	131586559	131586560	+	Intron	DEL	GT	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131586559_131586560delGT	uc004bwd.2	-						C9orf114_uc004bwe.2_Intron|C9orf114_uc010mym.2_Intron	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490												0						GAGCtgtgtggtgtgtgtgtgt	0.500													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	25056538	25056539	+	IGR	INS	-	TCCT	TCCT	rs147747455	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25056538_25056539insTCCT								ARHGAP21 (43941 upstream) : PRTFDC1 (81015 downstream)																							agaTACCTGGAtccttccttcc	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86535359	86535360	+	IGR	INS	-	TT	TT	rs138295367	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86535359_86535360insTT								FAM190B (257083 upstream) : GRID1 (823952 downstream)																							cgctctttttctttttcttttt	0.000													6	4	---	---	---	---	
FAM22D	728130	broad.mit.edu	37	10	89117852	89117854	+	5'UTR	DEL	AGA	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89117852_89117854delAGA	uc001kes.2	+	1					FAM22D_uc009xte.1_5'UTR	NM_001009610	NP_001009610	Q5VT03	FA22D_HUMAN	hypothetical protein LOC728130												0						GCTGTGAGTCAGAAGGACAATTT	0.483													5	5	---	---	---	---	
PDCD11	22984	broad.mit.edu	37	10	105159972	105159973	+	Intron	INS	-	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105159972_105159973insG	uc001kwy.1	+							NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11						mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GGAACATTGGCGGCCCCCCCCC	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93922330	93922330	+	IGR	DEL	A	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93922330delA								PANX1 (7195 upstream) : FOLR4 (116473 downstream)																							GAGCAGAAAGAAAAAAAAAAG	0.219													4	2	---	---	---	---	
MON2	23041	broad.mit.edu	37	12	62894781	62894783	+	Intron	DEL	TAT	-	-	rs113437686		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62894781_62894783delTAT	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_5'Flank|MON2_uc001srd.1_Intron	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TCAAAGGTAGTATTAAGATAGTT	0.207													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21835723	21835728	+	IGR	DEL	GGCGAG	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21835723_21835728delGGCGAG								MRP63 (82505 upstream) : ZDHHC20 (114782 downstream)																							GATGGACTGAGGCGAGGGGTGGGACT	0.646													3	3	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50176231	50176231	+	Intron	DEL	T	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50176231delT	uc010anj.1	-						KLHDC1_uc001www.2_Intron|KLHDC1_uc010tqg.1_Intron|KLHDC1_uc010tqh.1_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		ATTTTTGTGATTTTTTTTTTT	0.318													4	4	---	---	---	---	
HSPA2	3306	broad.mit.edu	37	14	65009534	65009535	+	3'UTR	INS	-	T	T	rs148978517	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65009534_65009535insT	uc001xhj.2	+	2					HSPA2_uc001xhk.3_3'UTR	NM_021979	NP_068814	P54652	HSP72_HUMAN	heat shock 70kDa protein 2						response to unfolded protein|spermatid development	cell surface	ATP binding|unfolded protein binding			skin(1)	1				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CTCTCTCTCTCTTTTTTTTTGT	0.411													3	3	---	---	---	---	
CCNDBP1	23582	broad.mit.edu	37	15	43481303	43481304	+	Intron	INS	-	AAAA	AAAA			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43481303_43481304insAAAA	uc001zqv.2	+						CCNDBP1_uc001zqu.2_Intron|CCNDBP1_uc010bdc.2_Intron|CCNDBP1_uc010bdb.2_Intron|CCNDBP1_uc010udl.1_Intron|CCNDBP1_uc001zqw.2_Intron|CCNDBP1_uc001zqx.2_Intron|CCNDBP1_uc010bdd.2_Intron|CCNDBP1_uc001zqy.2_Intron	NM_012142	NP_036274	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1 isoform 1						cell cycle	cytoplasm|nucleus	protein binding			ovary(1)|kidney(1)	2		all_cancers(109;3.31e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		aaaaaaaaaagaaaaagaaaga	0.149													8	7	---	---	---	---	
USP3	9960	broad.mit.edu	37	15	63829053	63829053	+	Intron	DEL	A	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63829053delA	uc002amf.2	+						USP3_uc010uii.1_Intron|USP3_uc002amg.2_Intron|USP3_uc002amh.2_Intron|USP3_uc010uij.1_Intron|USP3_uc010uik.1_Intron|USP3_uc010bgs.2_Intron|USP3_uc002ami.2_5'Flank	NM_006537	NP_006528	Q9Y6I4	UBP3_HUMAN	ubiquitin thiolesterase 3						DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)		actccgtctcaaaaaaaaaaa	0.100													4	2	---	---	---	---	
IGDCC3	9543	broad.mit.edu	37	15	65625356	65625357	+	Intron	INS	-	C	C	rs149190723	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65625356_65625357insC	uc002aos.2	-							NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule											ovary(3)	3						GGTATTGACGGACCCGGAGGGC	0.599													3	4	---	---	---	---	
PRSS53	339105	broad.mit.edu	37	16	31095418	31095419	+	Intron	INS	-	G	G			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31095418_31095419insG	uc002eaq.2	-						PRSS53_uc002ear.2_Intron	NM_001039503	NP_001034592	Q2L4Q9	PRS53_HUMAN	polyserase 3 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0						AGGGTTTGGCAGGAGGCCCCGG	0.559													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20648273	20648273	+	IGR	DEL	T	-	-	rs36007188		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20648273delT								LGALS9B (277425 upstream) : CCDC144NL (118437 downstream)																							AACACTAGACTTTTTTTTTTT	0.313													6	3	---	---	---	---	
CACNB1	782	broad.mit.edu	37	17	37347528	37347529	+	Intron	INS	-	ACTTATTAT	ACTTATTAT	rs138131266	by1000genomes	TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37347528_37347529insACTTATTAT	uc002hrm.1	-						CACNB1_uc002hrl.1_Intron|CACNB1_uc002hrn.2_Intron|CACNB1_uc002hro.2_Intron|CACNB1_uc002hrp.1_Intron|CACNB1_uc010web.1_Intron	NM_000723	NP_000714	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1						axon guidance	voltage-gated calcium channel complex				large_intestine(1)|ovary(1)	2					Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Verapamil(DB00661)	taataacacgcacttattatac	0.000													4	2	---	---	---	---	
PCTP	58488	broad.mit.edu	37	17	53848256	53848257	+	Intron	INS	-	T	T	rs71363819		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53848256_53848257insT	uc002iul.3	+						PCTP_uc002ium.3_Intron|PCTP_uc010dcg.2_Intron|PCTP_uc010dch.2_Intron	NM_021213	NP_067036	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein isoform 1							cytosol	phosphatidylcholine binding|phosphatidylcholine transmembrane transporter activity			lung(1)	1			BRCA - Breast invasive adenocarcinoma(1;0.00207)			gatttttttgcttttttttttt	0.000													3	3	---	---	---	---	
MFSD11	79157	broad.mit.edu	37	17	74766137	74766138	+	Intron	DEL	AG	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74766137_74766138delAG	uc002jta.2	+						MFSD11_uc002jtb.2_Intron|MFSD11_uc010dha.2_Intron|MFSD11_uc002jtc.2_Intron|MFSD11_uc002jtd.3_Intron|MFSD11_uc010dhb.2_Intron|MFSD11_uc002jte.2_Intron	NM_024311	NP_077287	O43934	MFS11_HUMAN	major facilitator superfamily domain containing							integral to membrane				ovary(1)	1						ttttccagacagagtctcgctc	0.084													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50554196	50554196	+	Intron	DEL	T	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50554196delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGAGCAGTTATTTTTTTTTTC	0.383													4	2	---	---	---	---	
IL12RB1	3594	broad.mit.edu	37	19	18188173	18188174	+	Intron	INS	-	A	A			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18188173_18188174insA	uc002nhw.1	-						IL12RB1_uc010xqb.1_Intron|IL12RB1_uc002nhx.1_Intron|IL12RB1_uc002nhy.2_Intron	NM_005535	NP_005526	P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1 isoform 1						cellular response to interferon-gamma|interleukin-12-mediated signaling pathway|positive regulation of activated T cell proliferation|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response	interleukin-12 receptor complex|interleukin-23 receptor complex	cytokine receptor activity			pancreas(1)	1						ctccgtctcagaaaaaaaaaaa	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31818936	31818936	+	IGR	DEL	A	-	-	rs140775761		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31818936delA								C20orf71 (3379 upstream) : PLUNC (4866 downstream)																							gagacagagcaagactaagaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32479566	32479566	+	IGR	DEL	T	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32479566delT								CHMP4B (37397 upstream) : RALY (102166 downstream)																							tctatctttcttttttctttc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37281795	37281797	+	IGR	DEL	ATG	-	-	rs112245163		TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37281795_37281797delATG								ADIG (64691 upstream) : SLC32A1 (71308 downstream)																							ggtgatgataatgatggtggtgg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39187194	39187195	+	IGR	DEL	GG	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39187194_39187195delGG								None (None upstream) : MAFB (127324 downstream)																							aaggaaggaaggaaggaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40410597	40410598	+	IGR	DEL	AC	-	-			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40410597_40410598delAC								CHD6 (163464 upstream) : PTPRT (290795 downstream)																							ATGTGCATGTacacacacacac	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13485646	13485647	+	IGR	INS	-	C	C			TCGA-A3-3346-01A-01D-0966-08	TCGA-A3-3346-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13485646_13485647insC								None (None upstream) : None (None downstream)																							cacaagtgttacatcacttagg	0.000													4	2	---	---	---	---	
